I am setting up a server for a local Habitat for Humanity. The
server has
2 drives and I was going to use the second drive as a backup. Then
I got
an idea, why not build the kernel with root on wd0a and clone the
drive?

If the first drive was to fail, then the second drive should work as a

stand alone. I found an example, but it wasn't from a NetBSD site.
I was

going to boot from the live cd and use:
dd if=/dev/wd0d of=/dev/wd1d bs=32k conv=noerror,sync

But from what I remember it was really easy to trash both hard
drives with

this and was wondering if this is the best way to do it.

I don't think it's generally recommended but you're certainly not
going to trash the source hard drive... Not sure where that piece of
FUD comes from.

In the past I've used rsync to backup root drives to backup drives...
You need to installboot on the second drive seperately and then --
exclude /boot... You can decide whether to use --delete... i've
always chosen to not use --delete just in case something goes nuts
and starts deleting files on my primary disk... Then I do --delete
manually occasionally...